Photoactive macromolecules and uses thereof

ABSTRACT

The present invention provides water soluble photoactive macromolecular complexes and methods for detecting an analyte in a sample by using a binding agent conjugated to a water soluble photoactive macromolecule.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.62/323,444, filed on Apr. 15, 2016, the contents of which areincorporated by reference herewith in their entirety.

FIELD OF THE INVENTION

This invention relates to complexes and methods for detecting analytesin a sample.

BACKGROUND OF THE INVENTION

Water soluble fluorescent polymers can be used in a variety ofbiological applications by generating signals which can be monitored inreal time and provide simple and rapid methods for the detection ofbiological targets and events.

Brightness of a dye is an overall contribution from the extinctioncoefficient (ε, measure of the amount of light absorbed at a particularwavelength) and fluorescence quantum yield (Φ, measure of the lightemitted in the form of radiation from its singlet excited state). Mostof the reported organic violet dyes such as coumarin, BODIPY, cyanine,squaraine etc are single molecules and shows relatively low extinctioncoefficient in the range of 10,000-70,000 M⁻¹cm⁻¹ at 405 nm. It has beenshown that molecules having multiple chromophores exhibit higher ε valuedue to the overall contribution from different chromophores. There arevarious reports on dendrimeric and polymeric backbone approaches where asingle molecule contains multiple chromophores.

However, many of the previously reported polymeric dyes are highlyhydrophobic and are used for material applications such as lightemitting diodes, solar cells etc. Consequently, many polymeric dyes arenot useful under aqueous conditions due to the poor solubility,brightness, and broadening of the spectra. Only a few reports deal withwater soluble fluorescent polymers for biological applications which areexcitable with a 405 nm and 355 nm laser. Therefore, identification ofnovel polymeric cores is needed in order to expand the arsenal of watersoluble polymeric dyes for biological applications, including for thedetection of analytes.

The present invention addresses these and other disadvantages of priorart complexes and methods for detecting analytes in a sample.

BRIEF SUMMARY OF THE INVENTION

The present invention generally provides novel, water solublefluorescent polymers and methods for detecting analytes in a sampleusing complexes comprising the fluorescent polymers conjugated tobinding agents.

In a first embodiment, the present invention provides a water solublefluorescent polymer having the structure of Formula I:

wherein;

each X is independently selected from the group consisting of a C andSi;

each Y is independently selected from the group consisting of a bond,CR¹R², and SiR¹R²;

when Y is a bond X is directly bonded to both rings;

each R¹ is independently selected from the group consisting ofpolyethylene glycol (PEG), ammonium alkyl salt, ammonium alkyloxy salt,ammonium oligoether salt, sulfonate alkyl salt, sulfonate alkoxy salt,sulfonate oligoether salt, sulfonamido oligoether, and

each R² is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, PEG, ammonium alkyl salt, ammonium alkyloxy salt,ammonium oligoether salt, sulfonate alkyl salt, sulfonate alkoxy salt,sulfonate oligoether salt, sulfonamido oligoether, and

each R³ is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, and PEG;

each Z is independently selected from the group consisting of C, O, andN;

each Q is independently selected from the group consisting of a bond,NH, NR⁴, and CH₂;

each M is independently an electron rich linker unit capable of alteringthe polymer band gap and is evenly or randomly distributed along thepolymer main chain and is each independently selected from the groupconsisting of

-   -   wherein,    -   each R⁴ is a non-ionic side group capable of imparting        solubility in water in excess if 10 mg/mL and is each        independently selected from the group consisting of halogen,        hydroxyl, C₁-C₁₂ alkyl, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂        cycloalkyl, C₁-C₁₂ haloalkyl, C₁-C₁₂ alkoxy, C₂-C₁₈        (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino,        (CH₂)_(x′)(OCH₂—CH₂)_(y′)OCH₃ where each x′ is independently an        integer from 0-20; each y′ is independently an integer from        0-50, and a C₂-C₁₈ (hetero)aryl group;

each optional linker L is an aryl or hetroaryl group evenly or randomlydistributed along the polymer main chain and are substituted with one ormore pendant chains terminated with a functional group selected from thegroup consisting of amine, carbamate, carboxylic acid, carboxylate,maleimide, activated ester, N-hydroxysuccinimidyl, hydrazine, hydrazide,hydrazone, azide, alkyne, aldehyde, thiol, and protected groups thereoffor conjugation to another substrate, acceptor dye, molecule or bindingagent;

each G¹ and G² are each independently selected from the group consistingof hydrogen, halogen, alkyne, optionally substituted aryl, optionallysubstituted heteroaryl, halogen substituted aryl, silyl, diazonium salt,triflate, acetyloxy, azide, sulfonate, phosphate, boronic acidsubstituted aryl, boronic ester substituted aryl, boronic ester, boronicacid, optionally substituted dihydrophenanthrene (DHP), optionallysubstituted fluorene, aryl or hetroaryl substituted with one or morependant chains terminated with a functional group selected from amine,carbamate, carboxylic acid, carboxylate, maleimide, activated ester,N-hydroxysuccinimidyl, hydrazine, hydrazide, hydrazone, azide, alkyne,aldehyde, thiol, and protected groups thereof for conjugation to asubstrate or a binding agent;

a, c, and d, define the mol % of each unit within the structure whicheach can be evenly or randomly repeated and where a is a mol % from 10to 100%, c is a mol % from 0 to 90%, and each d is a mol % from 0 to25%;

each b is independently 0 or 1;

m is an integer from 1 to about 10,000; and

each n is independently an integer from 1 to 20.

In some cases, the polymer has the structure of Formula II:

In some cases, the polymer has the structure of Formula III:

-   -   wherein, each f is independently an integer from 0 to 50 and        each R⁵ is independently selected from the group consisting of        H, C₁-C₁₂ alkyl, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂        cycloalkyl, C₁-C₁₂ haloalkyl, C₁-C₁₂ alkoxy, C₂-C₁₈        (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino, and C₁-C₁₂ alkoxy.

In some cases the polymer has the structure of Formula IV:

In some cases, the polymer has the structure of Formula V:

In some cases, the polymer is a copolymer and has the structure ofFormula VI:

wherein g and a together is a mol % from 10 to 100%.

In some cases, the polymer is a copolymer and has the structure ofFormula VII:

wherein, each g and a together is a mol % from 10 to 100%; and each f isindependently an integer from 0 to 50 and each R⁵ is independentlyselected from the group consisting of H, C₁-C₁₂ alkyl, C₂-C₁₂ alkene,C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁-C₁₂ haloalkyl, C₁-C₁₂ alkoxy,C₂-C₁₈ (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino, and C₁-C₁₂ alkoxy.

In some cases, the polymer is a copolymer has the structure of FormulaVIII:

In some cases, the polymer is a copolymer and has the structure ofFormula IX:

In some embodiments, L is each independently selected from the groupconsisting of

wherein,

each R⁶ is independently selected from the group consisting of H, OH,SH, NHCOO-t-butyl, (CH₂)_(n)COOH, (CH₂)_(n)COOCH₃, (CH₂)_(n)NH₂,(CH₂)_(n)NH—(CH₂)_(n)—CH₃, (CH₂)_(n)NHCOOH,(CH₂)_(n)NHCO—(CH₂)_(n)—CO—(CH₂)_(n)—CH₃, (CH₂)_(n)NHCOO—(CH₂)_(n)—CH₃,(CH₂)_(n)NHCOOC(CH₃)₃, (CH₂)_(n)NHCO(C₃-C₁₂)cycloalkyl,(CH₂)_(n)NHCO(CH₂CH₂O)_(f), (CH₂)_(n)NHCO(CH₂)_(n)COOH,(CH₂)_(n)NHCO(CH₂)_(n)COO(CH₂)_(n)CH₃, (CH₂)_(n)(OCH₂CH₂)_(f)OCH₃,N-maleimide, halogen, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl,C₁-C₁₂ halo alkyl, C₁-C₁₂ (hetero)aryl, C₁-C₁₂ (hetero)arylamino, andbenzyl optionally substituted with one or more halogen, hydroxyl, C₁-C₁₂alkoxy, or (OCH₂CH₂)_(f)OCH₃; each f is independently an integer from 0to 50; and each n is independently an integer from 1 to 20.

In some embodiments, G¹ and G² are each independently selected from thegroup consisting of optionally substituted dihydrophenanthrene (DHP),optionally substituted fluorene, aryl substituted with one or morependant chains terminated with a functional group, and a hetroarylsubstituted with one or more pendant chains terminated with a functionalgroup.

In some embodiments, G¹ and G² are each independently selected from thegroup consisting of

wherein,

each R⁶ is independently selected from the group consisting of H, OH,SH, NHCOO-t-butyl, (CH₂)_(n)COOH, (CH₂)_(n)COOCH₃, (CH₂)_(n)NH₂,(CH₂)_(n)NH—(CH₂)_(n)—CH₃, (CH₂)_(n)NHCOOH,(CH₂)_(n)NHCO—(CH₂)_(n)—CO—(CH₂)_(n)—CH₃, (CH₂)_(n)NHCOO—(CH₂)_(n)—CH₃,(CH₂)_(n)NHCOOC(CH₃)₃, (CH₂)_(n)NHCO(C₃-C₁₂)cycloalkyl,(CH₂)_(n)NHCO(CH₂CH₂O)_(f), (CH₂)_(n)NHCO(CH₂)_(n)COOH,(CH₂)_(n)NHCO(CH₂)_(n)COO(CH₂)_(n)CH₃, (CH₂)_(n)(OCH₂CH₂)_(f)OCH₃,N-maleimide, halogen, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl,C₁-C₁₂ halo alkyl, C₁-C₁₂ (hetero)aryl, C₁-C₁₂ (hetero)arylamino, andbenzyl optionally substituted with one or more halogen, hydroxyl, C₁-C₁₂alkoxy, or (OCH₂CH₂)_(f)OCH₃;

each f is independently an integer from 0 to 50; and

each n is independently an integer from 1 to 20.

In some embodiments, the present invention provides a method fordetecting an analyte in a sample comprising:

providing a sample that is suspected of containing the analyte;

contacting the sample with a binding agent conjugated to a water solublepolymer having the structure of Formula I:

wherein;

each X is independently selected from the group consisting of a C andSi;

each Y is independently selected from the group consisting of a bond,CR¹R², and SiR¹R²;

when Y is a bond X is directly bonded to both rings;

each R¹ is independently selected from the group consisting of ammoniumalkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, sulfonatealkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt,sulfonamido oligoether, and

each R² is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, PEG, ammonium alkyl salt, ammonium alkyloxy salt,ammonium oligoether salt, sulfonate alkyl salt, sulfonate alkoxy salt,sulfonate oligoether salt, sulfonamido oligoether, and

each R³ is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, and PEG;

each Z is independently selected from the group consisting of C, O, andN;

each Q is independently selected from the group consisting of a bond,NH, NR⁴, and CH₂;

-   -   each M is independently an electron rich linker unit capable of        altering the polymer band gap and is evenly or randomly        distributed along the polymer main chain and is each        independently selected from the group consisting of

-   -   wherein,    -   each R⁴ is a non-ionic side group capable of imparting        solubility in water in excess if 10 mg/mL and is each        independently selected from the group consisting of halogen,        hydroxyl, C₁-C₁₂ alkyl, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂        cycloalkyl, C₁-C₁₂ haloalkyl, C₁-C₁₂ alkoxy, C₂-C₁₈        (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino,        (CH₂)_(x′)(OCH₂—CH₂)_(y′)OCH₃ where each x′ is independently an        integer from 0-20; each y′ is independently an integer from        0-50, and a C₂-C₁₈ (hetero)aryl group;    -   each optional linker L is an aryl or hetroaryl group evenly or        randomly distributed along the polymer main chain and are        substituted with one or more pendant chains terminated with a        functional group selected from the group consisting of amine,        carbamate, carboxylic acid, carboxylate, maleimide, activated        ester, N-hydroxysuccinimidyl, hydrazine, hydrazide, hydrazone,        azide, alkyne, aldehyde, thiol, and protected groups thereof for        conjugation to another substrate, acceptor dye, molecule or        binding agent;

G¹ and G² are each independently selected from the group consisting ofhydrogen, halogen, alkyne, optionally substituted aryl, optionallysubstituted heteroaryl, halogen substituted aryl, silyl, diazonium salt,triflate, acetyloxy, azide, sulfonate, phosphate, boronic acidsubstituted aryl, boronic ester substituted aryl, boronic ester, boronicacid, optionally substituted dihydrophenanthrene (DHP), optionallysubstituted fluorene, aryl or hetroaryl substituted with one or morependant chains terminated with a functional group selected from amine,carbamate, carboxylic acid, carboxylate, maleimide, activated ester,N-hydroxysuccinimidyl, hydrazine, hydrazide, hydrazone, azide, alkyne,aldehyde, thiol, and protected groups thereof for conjugation to asubstrate or a binding agent;

a, c, and d define the mol % of each unit within the structure whicheach can be evenly or randomly repeated and where a is a mol % from 10to 100%, c is a mol % from 0 to 90%, and

each d is a mol % from 0 to 25%;

each b is independently 0 or 1;

m is an integer from 1 to about 10,000; and

each n is independently an integer from 1 to 20; and

wherein the binding agent is capable of interacting with the analyte ora target-associated biomolecule.

In some embodiments, the method further comprises, applying a lightsource to the sample that can excite the polymer; and detecting whetherlight is emitted from the conjugated polymer complex.

In some embodiments, the binding agent is a protein, peptide, affinityligand, antibody, antibody fragment, sugar, lipid, nucleic acid or anaptamer. In some embodiments, the binding agent is an antibody.

In some embodiments, the method is configured for flow cytometry. Insome embodiments, the binding agent is bound to a substrate. In someembodiments, the analyte is a protein expressed on a cell surface.

In some embodiments, the method is configured as a immunoassay. In someembodiments, the method further comprises providing additional bindingagents for detecting additional analytes simultaneously.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a comparison of fluorescence emission spectra of fluorene(FF), dihydrophenanthrene (DD) and fluorene-DHP (DF) polymers.

FIG. 2 shows the absorption spectra of both FF polymer and DD polymer.The graph shows absorption of the DD polymer (black curve) at 390 and410 nm, whereas the FF (grey curve) polymer shows the maxima around 401nm. Samples were measured under different concentration.

FIG. 3 shows the flow cytometric analysis of lysed whole blood stainedwith the new polymers-labeled anti-human CD4 and Pacific Blue-labeledCD4. The positive signal intensity of polymer dyes were nearly 5 timeshigher than Pacific Blue.

FIG. 4 shows the polymers of the present invention possess certainphysical and chemical characteristics of absorption, fluorescence,brightness, molecular weight, polydispersity, dye to protein ratio whenconjugated to an antibody etc. The preferred range of these parametersare shown in this table.

FIG. 5 shows the excitation and emission spectra of tandem polymers.Excitation was carried out at the polymer maxima (405 nm) and theemissions observed from the various acceptor dyes attached to thebackbone. Dye 1—FITC, Dye 2—Cy3B, Dye 3—Cy55.

DETAILED DESCRIPTION OF THE INVENTION I. General

The present invention provides novel, water soluble fluorescent polymersand methods for detecting analytes in a sample using complexescomprising the fluorescent polymers conjugated to binding agents. Thewater soluble conjugated polymers of present invention demonstratesignificantly increased brightness compared to other dyes.

II. Definitions

The abbreviations used herein have their conventional meaning within thechemical and biological arts.

As used herein, the term “ammonium” refers to a cation having theformula NHR₃ ⁺ where each R group, independently, is hydrogen or asubstituted or unsubstituted alkyl, aryl, aralkyl, or alkoxy group.Preferably, each of the R groups is hydrogen.

As used herein, “oligoether” is understood to mean an oligomercontaining structural repeat units having an ether functionality. Asused herein, an “oligomer” is understood to mean a molecule thatcontains one or more identifiable structural repeat units of the same ordifferent formula.

The term “sulfonate functional group” or “sulfonate,” as used herein,refers to both the free sulfonate anion (—S(═O)₂O—) and salts thereof.Therefore, the term sulfonate encompasses sulfonate salts such assodium, lithium, potassium and ammonium sulfonate.

The term “sulfonamido” as used herein refers to a group of formula—SO₂NR— where R is hydrogen, alkyl or aryl.

The term “alkyl” as used herein refers to a straight or branched,saturated, aliphatic radical having the number of carbon atomsindicated. For example, C₁-C₆ alkyl includes, but is not limited to,methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl,tert-butyl, pentyl, isopentyl, hexyl, etc. Other alkyl groups include,but are not limited to heptyl, octyl, nonyl, decyl, etc. Alkyl caninclude any number of carbons, such as 1-2, 1-3, 1-4, 1-5, 1-6, 1-7,1-8, 1-9, 1-10, 2-3, 2-4, 2-5, 2-6, 3-4, 3-5, 3-6, 4-5, 4-6 and 5-6. Thealkyl group is typically monovalent, but can be divalent, such as whenthe alkyl group links two moieties together.

The term “cycloalkyl” as used herein refers to a saturated or partiallyunsaturated, monocyclic, fused bicyclic or bridged polycyclic ringassembly containing from 3 to 12 ring atoms, or the number of atomsindicated monocyclic rings include, for example, cyclopropyl,cyclobutyl, cyclopentyl, cyclohexyl, and cyclooctyl. Bicyclic andpolycyclic rings include, for example, norbornane, decahydronaphthaleneand adamantane. For example, C₃₋₈cycloalkyl includes cyclopropyl,cyclobutyl, cyclopentyl, cyclohexyl, cyclooctyl, and norbornane.

The term “haloalkyl” as used herein refers to alkyl as defined abovewhere some or all of the hydrogen atoms are substituted with halogenatoms. Halogen (halo) preferably represents chloro or fluoro, but mayalso be bromo or iodo. For example, haloalkyl includes trifluoromethyl,flouromethyl, 1,2,3,4,5-pentafluoro-phenyl, etc. The term “perfluoro”defines a compound or radical which has at least two available hydrogenssubstituted with fluorine. For example, perfluorophenyl refers to1,2,3,4,5-pentafluorophenyl, perfluoromethane refers to1,1,1-trifluoromethyl, and perfluoromethoxy refers to1,1,1-trifluoromethoxy.

As used herein, the term “halogen” refers to fluorine, chlorine, bromineand iodine.

The term “alkoxy” as used herein refers to an alkyl group, as definedabove, having an oxygen atom that connects the alkyl group to the pointof attachment. Alkoxy groups include, for example, methoxy, ethoxy,propoxy, iso-propoxy, butoxy, 2-butoxy, iso-butoxy, sec-butoxy,tert-butoxy, pentoxy, hexoxy, etc. The alkoxy groups can be furthersubstituted with a variety of substituents described within. Forexample, the alkoxy groups can be substituted with halogens to form a“halo-alkoxy” group.

The term “alkene” as used herein refers to either a straight chain orbranched hydrocarbon, having at least one double bond. Examples ofalkene groups include, but are not limited to, vinyl, propenyl,isopropenyl, 1-butenyl, 2-butenyl, isobutenyl, butadienyl, 1-pentenyl,2-pentenyl, isopentenyl, 1,3-pentadienyl, 1,4-pentadienyl, 1-hexenyl,2-hexenyl, 3-hexenyl, 1,3-hexadienyl, 1,4-hexadienyl, 1,5-hexadienyl,2,4-hexadienyl, or 1,3,5-hexatrienyl. The alkene group is typicallymonovalent, but can be divalent, such as when the alkenyl group linkstwo moieties together.

The term “alkyne” as used herein refers to either a straight chain orbranched hydrocarbon, having at least one triple bond. Examples ofalkynyl groups include, but are not limited to, acetylenyl, propynyl,1-butynyl, 2-butynyl, isobutynyl, sec-butynyl, butadiynyl, 1-pentynyl,2-pentynyl, isopentynyl, 1,3-pentadiynyl, 1,4-pentadiynyl, 1-hexynyl,2-hexynyl, 3-hexynyl, 1,3-hexadiynyl, 1,4-hexadiynyl, 1,5-hexadiynyl,2,4-hexadiynyl, or 1,3,5-hexatriynyl. The alkynyl group is typicallymonovalent, but can be divalent, such as when the alkynyl group linkstwo moieties together.

The term “aryl” as used herein refers to a monocyclic or fused bicyclic,tricyclic or greater, aromatic ring assembly containing 6 to 16 ringcarbon atoms. For example, aryl may be phenyl, benzyl or naphthyl,preferably phenyl. “Arylene” means a divalent radical derived from anaryl group. Aryl groups can be mono-, di- or tri-substituted by one, twoor three radicals selected from alkyl, alkoxy, aryl, hydroxy, halogen,cyano, amino, amino-alkyl, trifluoromethyl, alkylenedioxy andoxy-C₂-C₃-alkylene; all of which are optionally further substituted, forinstance as hereinbefore defined; or 1- or 2-naphthyl; or 1- or2-phenanthrenyl. Alkylenedioxy is a divalent substitute attached to twoadjacent carbon atoms of phenyl, e.g. methylenedioxy or ethylenedioxy.Oxy-C₂-C₃-alkylene is also a divalent substituent attached to twoadjacent carbon atoms of phenyl, e.g. oxyethylene or oxypropylene. Anexample for oxy-C₂-C₃-alkylene-phenyl is 2,3-dihydrobenzofuran-5-yl.

Preferred as aryl is naphthyl, phenyl or phenyl mono- or disubstitutedby alkoxy, phenyl, halogen, alkyl or trifluoromethyl, especially phenylor phenyl-mono- or disubstituted by alkoxy, halogen or trifluoromethyl,and in particular phenyl.

The term “aryloxy” as used herein refers to a O-aryl group, wherein arylis as defined above. An aryloxy group can be unsubstituted orsubstituted with one or two suitable substituents. The term “phenoxy”refers to an aryloxy group wherein the aryl moiety is a phenyl ring. Theterm “heteroaryloxy” as used herein means an —O-heteroaryl group,wherein heteroaryl is as defined below. The term “(hetero)aryloxy” isuse to indicate the moiety is either an aryloxy or heteroaryloxy group.

The terms “Polyethylene glycol” or “PEG” as used herein refer to thefamily of biocompatible water-solubilizing linear polymers based on theethylene glycol monomer unit.

The term “heteroaryl” as used herein refers to a monocyclic or fusedbicyclic or tricyclic aromatic ring assembly containing 5 to 16 ringatoms, where from 1 to 4 of the ring atoms are a heteroatom each N, O orS. For example, heteroaryl includes pyridyl, indolyl, indazolyl,quinoxalinyl, quinolinyl, isoquinolinyl, benzothienyl, benzofuranyl,furanyl, pyrrolyl, thiazolyl, benzothiazolyl, oxazolyl, isoxazolyl,triazolyl, tetrazolyl, pyrazolyl, imidazolyl, thienyl, or any otherradicals substituted, especially mono- or di-substituted, by e.g. alkyl,nitro or halogen. Pyridyl represents 2-, 3- or 4-pyridyl, advantageously2- or 3-pyridyl. Thienyl represents 2- or 3-thienyl. Quinolinylrepresents preferably 2-, 3- or 4-quinolinyl. Isoquinolinyl representspreferably 1-, 3- or 4-isoquinolinyl. Benzopyranyl, benzothiopyranylrepresents preferably 3-benzopyranyl or 3-benzothiopyranyl,respectively. Thiazolyl represents preferably 2- or 4-thiazolyl, andmost preferred, 4-thiazolyl. Triazolyl is preferably 1-, 2- or5-(1,2,4-triazolyl). Tetrazolyl is preferably 5-tetrazolyl.

Preferably, heteroaryl is pyridyl, indolyl, quinolinyl, pyrrolyl,thiazolyl, isoxazolyl, triazolyl, tetrazolyl, pyrazolyl, imidazolyl,thienyl, furanyl, benzothiazolyl, benzofuranyl, isoquinolinyl,benzothienyl, oxazolyl, indazolyl, or any of the radicals substituted,especially mono- or di-substituted.

Similarly, substituents for the aryl and heteroaryl groups are variedand are selected from: -halogen, —OR′, —OC(O)R′, —NR′R″, —SR′, —R′, —CN,—NO₂, —CO₂R′, —CONR′R″, —C(O)R′, —OC(O)NR′R″, —NR″C(O)R′, —NR″C(O)₂R′,—NR′—C(O)NR″R′″, —NH—C(NH₂)═NH, —NR′C(NH₂)═NH, —NH—C(NH₂)═NR′, —S(O)R′,—S(O)₂R′, —S(O)₂NR′R″, —N₃, —CH(Ph)₂, perfluoro(C₁-C₄)alkoxy, andperfluoro(C₁-C₄)alkyl, in a number ranging from zero to the total numberof open valences on the aromatic ring system; and where R′, R″ and R′″are independently selected from hydrogen, (C₁-C₅)alkyl and heteroalkyl,unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C₁-C₄)alkyl,and (unsubstituted aryl)oxy-(C₁-C₄)alkyl.

Two of the substituents on adjacent atoms of the aryl or heteroaryl ringmay optionally be replaced with a substituent of the formula-T-C(O)—(CH₂)_(q)—U—, wherein T and U are independently —NH—, —O—, —CH₂—or a single bond, and q is an integer of from 0 to 2. Alternatively, twoof the substituents on adjacent atoms of the aryl or heteroaryl ring mayoptionally be replaced with a substituent of the formula-A-(CH₂)_(r)—B—, wherein A and B are independently —CH₂—, —O—, —NH—,—S—, —S(O)—, —S(O)₂—, —S(O)₂NR′— or a single bond, and r is an integerof from 1 to 3. One of the single bonds of the new ring so formed mayoptionally be replaced with a double bond. Alternatively, two of thesubstituents on adjacent atoms of the aryl or heteroaryl ring mayoptionally be replaced with a substituent of the formula—(CH₂)_(s)—X—(CH₂)_(t)—, where s and t are independently integers offrom 0 to 3, and X is —O—, —NR′—, —S—, —S(O)—, —S(O)₂—, or —S(O)₂NR′—.The substituent R′ in —NR′— and —S(O)₂NR′— is selected from hydrogen orunsubstituted (C₁-C₆)alkyl.

The term “(hetero)arylamino” as used herein refers an amine radicalsubstituted with an aryl group (e.g., —NH-aryl). An arylamino may alsobe an aryl radical substituted with an amine group (e.g., -aryl-NH₂).Arylaminos may be substituted or unsubstituted.

The term “amine” as used herein refers to an alkyl groups as definedwithin, having one or more amino groups. The amino groups can beprimary, secondary or tertiary. The alkyl amine can be furthersubstituted with a hydroxy group. Amines useful in the present inventioninclude, but are not limited to, ethyl amine, propyl amine, isopropylamine, ethylene diamine and ethanolamine. The amino group can link thealkyl amine to the point of attachment with the rest of the compound, beat the omega position of the alkyl group, or link together at least twocarbon atoms of the alkyl group. One of skill in the art will appreciatethat other alkyl amines are useful in the present invention.

The term “carbamate” as used herein refers to the functional grouphaving the structure —NR″CO₂R′, where R′ and R″ are independentlyselected from hydrogen, (C₁-C₈)alkyl and heteroalkyl, unsubstituted aryland heteroaryl, (unsubstituted aryl)-(C₁-C₄)alkyl, and (unsubstitutedaryl)oxy-(C₁-C₄)alkyl. Examples of carbamates include t-Boc, Fmoc,benzyloxy-carbonyl, alloc, methyl carbamate, ethyl carbamate,9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluorenylmethylcarbamate, Tbfmoc, Climoc, Bimoc, DBD-Tmoc, Bsmoc, Troc, Teoc,2-phenylethyl carbamate, Adpoc, 2-chloroethyl carbamate,1,1-dimethyl-2-haloethyl carbamate, DB-t-BOC, TCBOC, Bpoc, t-Bumeoc,Pyoc, Bnpeoc, V-(2-pivaloylamino)-1,1-dimethylethyl carbamate, NpSSPeoc.

The term “carboxylate” as used herein refers to the conjugate base of acarboxylic acid, which generally can be represented by the formula RCOO.For example, the term “magnesium carboxylate” refers to the magnesiumsalt of the carboxylic acid.

The term “activated ester” as used herein refers to carboxyl-activatinggroups employed in peptide chemistry to promote facile condensation of acarboxyl group with a free amino group of an amino acid derivative.Descriptions of these carboxyl-activating groups are found in generaltextbooks of peptide chemistry; for example K. D. Kopple, “Peptides andAmino Acids”, W. A. Benjamin, Inc., New York, 1966, pp. 50-51 and E.Schroder and K. Lubke, “The Peptides”; Vol. 1, Academic Press, New York,1965, pp. 77-128.

The terms “hydrazine” and “hydrazide” refer to compounds that containsingly bonded nitrogens, one of which is a primary amine functionalgroup.

The term “aldehyde” as used herein refers to a chemical compound thathas an —CHO group.

The term “thiol” as used herein refers to a compound that contains thefunctional group composed of a sulfur-hydrogen bond. The generalchemical structure of the thiol functional group is R—SH, where Rrepresents an alkyl, alkene, aryl, or other carbon-containing group ofatoms.

The term “silyl” as used herein refers to Si(R^(z))₃ wherein each R^(z)independently is alkyl aryl or other carbon-containing group of atoms.

The term “diazonium salt” as used herein refers to a group of organiccompounds with a structure of R—N₂ ⁺X⁻, wherein R can be any organicresidue (e.g., alkyl or aryl) and X is an inorganic or organic anion(e.g., halogen).

The term “triflate” also referred to as trifluoromethanesulfonate, is agroup with the formula CF₃SO₃.

The term “boronic acid” as used herein refers to a structure —B(OH)₂. Itis recognized by those skilled in the art that a boronic acid may bepresent as a boronate ester at various stages in the synthesis of thequenchers. Boronic acid is meant to include such esters. The term“boronic ester” or “boronate ester” as used herein refers to a chemicalcompound containing a —B(Z¹)(Z²) moiety, wherein Z¹ and Z² together forma moiety where the atom attached to boron in each case is an oxygenatom. In some embodiments, the boronic ester moiety is a 5-memberedring. In some other embodiments, the boronic ester moiety is a6-membered ring. In some other embodiments, the boronic ester moiety isa mixture of a 5-membered ring and a 6-membered ring.

III. Compositions Polymers

The compounds of the present invention comprise water solublefluorescent polymers having the structure of Formulas I-XIII. In someembodiments, polymers of the present invention utilizedihydrophenanthrene (DHP), fluorene, and combinations of DHP andfluorene monomers as shown in Formula I:

The polymers complexes of the present invention can contain unitscapable of altering the polymer band gap and are evenly or randomlydistributed along the polymer main chain. These unites are representedin Formula I as M. The polymers complexes of the present invention canalso contain linkers represented in Formula I as L. Each optional linkerL is an aryl or hetroaryl group evenly or randomly distributed along thepolymer main chain and are substituted with one or more pendant chainsterminated with a functional group selected from the group consisting ofamine, carbamate, carboxylic acid, carboxylate, maleimide, activatedester, N-hydroxysuccinimidyl, hydrazine, hydrazide, hydrazone, azide,alkyne, aldehyde, thiol, and protected groups thereof for conjugation toa substrate or binding agent.

The polymers complexes of the present invention also contain cappingunits represented in Formula I as each G¹ and G², which are eachindependently selected from the group consisting of hydrogen, halogen,alkyne, optionally substituted aryl, optionally substituted heteroaryl,halogen substituted aryl, silyl, diazonium salt, triflate, acetyloxy,azide, sulfonate, phosphate, boronic acid substituted aryl, boronicester substituted aryl, boronic ester, boronic acid, optionallysubstituted dihydrophenanthrene (DHP), optionally substituted fluorene,aryl or hetroaryl substituted with one or more pendant chains terminatedwith a functional group selected from amine, carbamate, carboxylic acid,carboxylate, maleimide, activated ester, N-hydroxysuccinimidyl,hydrazine, hydrazide, hydrazone, azide, alkyne, aldehyde, thiol, andprotected groups thereof for conjugation to a substrate or bindingagent.

In some cases, the polymer has the structure of Formula II:

In some cases the polymer has the structure of Formula IV:

In some cases, the polymer has the structure of Formula V:

In some cases, the polymer is a copolymer and has the structure ofFormula VI:

In some cases, the polymer is a copolymer and has the structure ofFormula VII:

In some embodiments, the polymer has acceptor dyes attached to thebackbone that will allow to excite the polymer backbone and see monitorthe emission of the acceptor dyes attached to the back bone throughenergy transfer. Acceptor dyes useful in the invention include FITC,CY3B, Cy55, Alexa 488, Texas red, Cy5, Cy7, Alexa 750, and 800CW. Forexample, polymers with acceptor dyes of the present invention include:

Monomers

Monomers of the present invention include dihydrophenanthrene (DHP) andfluorene based monomers. For example, monomers of the present inventioninclude:

Where both terminal ends of the monomers are independently or both ahalogen atom, boronic ester or boronic acid, silyl, diazonium salt,triflate, acetyloxy, sulfonate, or phosphate which can undergo Pd orNickel salt catalyzed polymerization reactions. R¹ is independently aside group capable of imparting solubility in water/buffer and each R¹is independently selected from the group consisting of ammonium alkylsalt, ammonium alkyloxy salt, ammonium oligoether salt, sulfonate alkylsalt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamidooligoether, and

each R² is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, PEG, ammonium alkyl salt, ammonium alkyloxy salt,ammonium oligoether salt, sulfonate alkyl salt, sulfonate alkoxy salt,sulfonate oligoether salt, sulfonamido oligoether, and

each R³ is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, and PEG; each Z is independently selected from thegroup consisting of C, O, and N; each Q is independently selected fromthe group consisting of a bond, NH, NR⁴ and CH₂; and each R⁵ isindependently selected from the group consisting of H, C₁-C₁₂ alkyl,C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁-C₁₂ haloalkyl,C₁-C₁₂ alkoxy, C₂-C₁₈ (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino, andC₁-C₁₂ alkoxy.

In some embodiments, monomers of the present invention also includebridged monomers. For example, bridged monomers of the present inventioninclude:

Synthesis

DHP monomers of the present invention can be made as shown below.

For example, 2,7-dibromo-trans-9,10-dihydrophenanthrene-9,10-diol(DHP—OH) can be prepared as follows. In a conical flask (2000 L), addabout 26 g of NaBH₄ into a stirring water-ethanol mixture (120 mL+780mL). To this solution, add about 24 g of 2,7-dibromophenanthrene,9,10-dione portion-wise but quickly (in 5 min). The reaction mix allowedstirring for a day. The color of the solution changes from orange red topale yellow to white by the end of the reaction. Stop the reaction andneutralize the reaction mixture with dil HCl acid. After theneutralization, filter the white precipitate and wash with excess water.Thus obtained white precipitate was washed with very cold (<−15° C.)ethanol (100 mL) and Methanol (100 mL).

DHP—OSO₃H can be prepared as follows. In a 2 neck round bottom flask,DHP—OH (3.6 g) and 18C6 (500 mg) were dissolved in 120 mL of THF. Thesolution was purged with nitrogen (20 min) and NaH (2 g) was added whilenitrogen purging continues. The color of the solution changes fromcolorless to pale pink, dark pink, brown and dark green in 10-15 min. Inanother RB, 12 g of 1,3 propane sultone was dissolved in 20 mL of THFand nitrogen purged. This sultone solution was added to DHP—OH solutionby addition funnel over a period of 20-30 minutes. The reaction wasstirred at RT for 4-5 hrs. The solvents were evaporated, and dissolvedthe precipitate in water. Acetone was added to obtain white precipitateof DPS in the form of disodium salt. Filter the precipitate andredissolve in water (minimal amount) neutralize with HCl and precipitateagain in acetone. Repeated precipitation (2-3 times) followed bycentrifugation gives DPS as white solid.

DHP—OSO₂Cl can be prepared as follows. 5 g of DHP—OSO₃H was taken in around bottom flask and mixed with 25 mL of DMF. To this about 10 mL ofSOCl₂ was added dropwise and the mixture allowed to stir for overnight.Next morning, reaction mixture was poured into 200 mL water andprecipitate was filtered and dried.

DHP-sulfonamide PEG can be prepared as follows. DHP—OSO₂Cl was mixedwith 2.2 equivalent of PEG amine in dichloromethane/TEA mixture. After 3h sonication reaction the crude product was extracted in dichloromethanefollowed by column chromatography (silica gel, MeOH—CHCl₃).

Diboronic ester of DHP-sulfonamide PEG can be prepared as follows. Thedibromo compound was mixed with DMSO under nitrogen and to this 3equivalent of bispinacolatodiboron was added. The reagents were reactedwith 12 equivalent of potassium acetate and 4 equivalent of Pd(dppf)Cl₂catalyst for 5 hours at 80deg. Reaction mixture cooled down andextracted with CHCl3/water. The organic layer was concentrated andpurified by column chromatography (silica gel, MeOH—CHCl₃).

Similarly, Fluorene monomers of the present invention can be made asdescribed below. For example, FL-OSO₃H can be prepared as follows. In a2 neck round bottom flask, 5 g of Fluorene was mixed with in 70 of DMSO.The solution was purged with nitrogen (20 min) and 50% NaOH (12 eq) wasadded while nitrogen purging continues. The color of the solutionchanges from colorless to dark brown. Propane sultone (3 eq) was weighedand dissolved in DMSO. This was added to the fluorene reaction mixturedropwise over a period of 5 minutes. The reaction was stirred at RT for4-5 hrs. The solvents were evaporated, and dissolved the precipitate inwater. Acetone was added to obtain white precipitate of DPS in the formof disodium salt. Filter the precipitate and redissolve in water(minimal amount) neutralize with HCl and precipitate again in acetone.Repeated precipitation (2-3 times) followed by centrifugation givesFL-OSO₃H as white solid.

FL-OSO₂Cl can be prepared as follows. 5 g of FL-OSO₃H was taken in around bottom flask and mixed with 25 mL of DMF. To this about 10 mL ofSOCl₂ was added dropwise and the mixture allowed to stir for overnight.Next morning, reaction mixture was poured into 200 mL water andprecipitate was filtered and dried.

FL-sulfonamide PEG can be prepared as follows. FL-OSO₂Cl was mixed with2.2 equivalent of PEG amine in dichloromethane/TEA mixture. After 3 hsonication reaction the crude product was extracted in dichloromethanefollowed by column chromatography (silica gel, MeOH—CHCl₃).

Diboronic ester of FL-sulfonamide PEG can be prepared as follows. Thedibromo compound was mixed with DMSO under nitrogen and to this 3equivalent of bispinacolatodiboron was added. The reagents were reactedwith 12 equivalent of potassium acetate and 4 equivalent of Pd(dppf)Cl₂catalyst for 5 hours at 80deg. Reaction mixture cooled down andextracted with CHCl₃/water. The organic layer was concentrated andpurified by column chromatography (silica gel, MeOH—CHCl₃).

Polymerization

The compounds described in the above embodiments may be made usingprocedures known in the art. In some embodiments, fluorescent polymerscan be made from dihydrophenanthrene (DHP) monomers combined withelectron rich linker units. In some embodiments, bright polymeric dyescan be made from fluorene monomers combined with electron rich linkerunits. In some embodiments, bright polymeric dyes can be made from acombination of DHP and fluorene monomers combined with electron richlinker units.

Generally, polymerization monomer units described above can beaccomplished using polymerization techniques known to those of skill inthe art or using methods known in the art in combination with methodsdescribed herein. For example, Synthesis of diboronic ester derivativesfrom a dihalide monomer can be accomplished via Suzuki coupling withbis(pinacolato) diboron:

Similarly, polymerization can also be achieved via Suzuki coupling:

Where J¹ and J² are independently H, Br, B(OH)₂, or a boronic ester.

For example, polymerization can proceed as follows. In a round bottomflask both the bromo and boronic monomers were taken in (DMF-water)mixture and purged with nitrogen for 10 minutes. Under nitrogen about 20equivalent of CsF and 10% of Pd(OAc)2 were mixed and heated at 800Celcius. Polymerization was monitored using UV-Vis spectroscopy and SECchromatography. Later to the reaction mixture, a capping agent (selectedfrom G1) containing appropriate functional group was added and 3 hourslater the second capping agent (selected from G2) added. After thereaction the crude reaction mixture was evaporated off and passedthrough a gel filtration column to remove small organic molecules andlow MW oligomers.

Capping Units

Linkers and capping units can be conjugated to a polymer backbone ofthis invention via similar mechanisms as described previously. Forexample, bromo- and boronic esters of capping units can be used toappend one or both ends of a polymer. Utilizing both bromo- and boronicesters of capping units will append both ends of polymer. Utilizing onlyone form, either a bromo- or boronic ester of a capping unit, willappend only those ends terminated with its respective complement and forsymmetric polymerizations can be used to statistically modify only oneend of a polymer. For asymmetric polymers this approach is used tochemically ensure the polymers are only modified at a single chainterminus. Capping units can also be appended asymmetrically by firstreacting a bromo-capping unit with a polymer with Y ends andsubsequently reacting the polymer with a boronic ester capping unit.

For example, capping agents of the present invention can be made asshown below.

Binding Agents

A “binding agent” of the invention can be any molecule or complex ofmolecules capable of specifically binding to target analyte. A bindingagent of the invention includes for example, proteins, small organicmolecules, carbohydrates (including polysaccharides), oligonucleotides,polynucleotides, lipids, affinity ligand, antibody, antibody fragment,an aptamer and the like. In some embodiments, the binding agent is anantibody or fragment thereof. Specific binding in the context of thepresent invention refers to a binding reaction which is determinative ofthe presence of a target analyte in the presence of a heterogeneouspopulation. Thus, under designated assay conditions, the specifiedbinding agents bind preferentially to a particular protein or isoform ofthe particular protein and do not bind in a significant amount to otherproteins or other isoforms present in the sample.

When the binding agents are antibodies, they may be monoclonal orpolyclonal antibodies. The term antibody as used herein refers toimmunoglobulin molecules and immunologically active portions ofimmunoglobulin (Ig) molecules. Such antibodies include, but are notlimited to, polyclonal, monoclonal, mono-specific polyclonal antibodies,antibody mimics, chimeric, single chain, Fab, Fab′ and F(ab′)₂fragments, Fv, and an Fab expression library.

Complexes

In general, fluorescent polymers of the present invention can beconjugated to binding agents using techniques known to those of skill inthe art or using methods known in the art in combination with methodsdescribed herein.

For example, preparation of polymer NHS ester can proceed as follows.Take 5 mg of the polymer in a clean vial and dissolve in 1 mL dry CH₃CN.To this add 15 mg TSTU and stir for 2 more minutes. To this add 100 uLDIPEA and continue stirring for overnight with the cap sealed withparafilm. Later evaporate off the organic solvents in the reactionmixture Dissolve the crude NHS in about 750 uL of 1×BBS buffer (pH 8.8)by a quick vortex and transfer it to the Zeba column 40K MWCO. Spin downthe sample at 2200 RPM for 2 min and use this polymer NHS immediately.

Conjugation of polymer NHS with CD4 can proceed as follows. Take thepolymer NHS in 1×BBS (˜800 uL) which was spun down, add to 0.6 mg of CD4and mix with 100 uL of 0.5M Borate buffer (pH 9.0). Vortex quickly for30 seconds and allow to mix for 3-4 hours in the coulter mix.

Purification of conjugate through Histrap HP column can proceed asfollows. Approach 1: After the crude reaction purify the conjugate usinga Histrap HP column. Load the sample using 1×PBS buffer and collect theunbound fraction. This can be done using 20 CV of buffer. Later changethe buffer to wash the bound fraction which has both conjugate and freeantibody. This can be done using 1×PBS with 0.25M imidazole running for10 CV.

Approach 2: Hitrap SP Sepharose FF column. Equilibrate the column andload the sample using 20 mM Citrate buffer pH 3.5 and collect theunbound fraction. This can be done using 20 CV of buffer. Later changethe buffer to elute the bound fraction which has both conjugate and freeantibody. This can be done using 20 mM Tris buffer pH 8.5 running for 20CV.

Approach 3: Load the crude conjugate in a Tangential flow filtrationsystem equipped with a 300K MWCO membrane. The conjugate is washed using1×PBS until the filtrate show no absorption at 405 nm. Later thecompound is concentrated.

Purification of conjugate through SEC column can proceed as follows.Load the crude conjugate containing free antibody to the Size ExclusionColumn, using 1×PBS. Pool the tubes after checking the absorptionspectra and concentrate in a Amicon Ultra-15 having a 30 KDa MWCOcentrifugal concentrator.

IV. Methods of Detecting an Analyte Overview

The present invention provides a method for detecting an analyte in asample comprising: providing a sample that is suspected of containing ananalyte; providing a conjugated polymer complex, which comprises abinding agent conjugated to a water soluble conjugated polymer. Thebinding agent is capable of interacting with the analyte. A light sourceis applied to the sample that can excite the polymer and light emittedfrom the conjugated polymer complex is detected. In the typical assay,fluorescent polymers of the invention are excitable with a light havingwavelength between about 395 nm and about 415 nm. The emitted light istypically between about 415 nm and about 475 nm. Alternatively,excitation light can have a wavelength between about 340 nm and about370 nm and the emitted light is between about 390 nm and about 420 nm.

Sample

The sample in the methods of the present invention can be, for example,blood, bone marrow, spleen cells, lymph cells, bone marrow aspirates (orany cells obtained from bone marrow), urine (lavage), serum, saliva,cerebral spinal fluid, urine, amniotic fluid, interstitial fluid, feces,mucus, or tissue (e.g., tumor samples, disaggregated tissue,disaggregated solid tumor). In certain embodiments, the sample is ablood sample. In some embodiments, the blood sample is whole blood. Thewhole blood can be obtained from the subject using standard clinicalprocedures. In some embodiments, the sample is a subset of one or morecells of whole blood (e.g., erythrocyte, leukocyte, lymphocyte (e.g., Tcells, B cells or NK cells), phagocyte, monocyte, macrophage,granulocyte, basophil, neutrophil, eosinophil, platelet, or any cellwith one or more detectable markers). In some embodiments, the samplecan be from a cell culture.

The subject can be a human (e.g., a patient suffering from a disease), acommercially significant mammal, including, for example, a monkey, cow,or horse. Samples can also be obtained from household pets, including,for example, a dog or cat. In some embodiments, the subject is alaboratory animal used as an animal model of disease or for drugscreening, for example, a mouse, a rat, a rabbit, or guinea pig.

Analytes

An “analyte” as used herein, refers to a substance, e.g., molecule,whose abundance/concentration is determined by some analyticalprocedure. For example, in the present invention, an analyte can be aprotein, peptide, nucleic acid, lipid, carbohydrate or small molecule.

The target analyte may be, for example, nucleic acids (DNA, RNA, mRNA,tRNA, or rRNA), peptides, polypeptides, proteins, lipids, ions,monosaccharides, oligosaccharides, polysaccharides, lipoproteins,glycoproteins, glycolipids, or fragments thereof. In some embodiments,the target analyte is a protein and can be, for example, a structuralmicrofilament, microtubule, and intermediate filament proteins,organelle-specific markers, proteasomes, transmembrane proteins, surfacereceptors, nuclear pore proteins, protein/peptide translocases, proteinfolding chaperones, signaling scaffolds, ion channels and the like. Theprotein can be an activatable protein or a protein differentiallyexpressed or activated in diseased or aberrant cells, including but notlimited to transcription factors, DNA and/or RNA-binding and modifyingproteins, nuclear import and export receptors, regulators of apoptosisor survival and the like.

Assays

Assay systems utilizing a binding agent and a fluorescent label toquantify bound molecules are well known. Examples of such systemsinclude flow cytometers, scanning cytometers, imaging cytometers,fluorescence microscopes, and confocal fluorescent microscopes.

In some embodiments, flow cytometry is used to detect fluorescence. Anumber of devices suitable for this use are available and known to thoseskilled in the art. Examples include BCI Navios, Gallios, Aquios, andCytoFLEX flow cytometers.

In other embodiments, the assay is an immunoassay. Examples ofimmunoassays useful in the invention include, but are not limited to,fluoroluminescence assay (FLA), and the like. The assays can also becarried out on protein arrays.

When the binding agents are antibodies, antibody or multiple antibodysandwich assays can also be used. A sandwich assay refers to the use ofsuccessive recognition events to build up layers of various bindingagents and reporting elements to signal the presence of a particularanalyte. Examples of sandwich assays are disclosed in U.S. Pat. No.4,486,530 and in the references noted therein.

V. Examples Example 1: Preparation of DHP Polymer Complex

Method 1: In a round bottom flask both the dibromo DHP and diboronic DHPmonomers (1:1) were taken in (DMF-water) mixture and purged withnitrogen for 10 minutes. Under nitrogen about 20 equivalent of CsF and10% of Pd(OAc)2 were mixed and heated at 80deg Celsius. Polymerizationwas monitored using UV-Vis spectroscopy and SEC chromatography. Later tothe reaction mixture, a capping agent (selected from G1) containingappropriate functional group was added and 3 hours later the secondcapping agent (selected from G2) added. After the reaction the crudereaction mixture was evaporated off and passed through a gel filtrationcolumn to remove small organic molecules and low MW oligomers. Later thecrude polymer passed through a Tangential flow filtration systemequipped with a 100K MWCO membrane. It is washed using 20% ethanol untilthe absorption of the filtrate diminishes.

Method 2: Alternatively, the polymerization can be done byself-polymerizing a bromo-boronic ester of DHP molecule. In a roundbottom flask DHP bromoboronic ester was taken in (DMF-water) mixture andpurged with nitrogen for 10 minutes. Under nitrogen about 10 equivalentof CsF and 5% of Pd(OAc)₂ were mixed and heated at 80deg Celsius.Polymerization was monitored using UV-Vis spectroscopy and SECchromatography. Later to the reaction mixture, a capping agent (selectedfrom G1) containing appropriate functional group was added and 3 hourslater the second capping agent (selected from G2) added. After thereaction the crude reaction mixture was evaporated off and passedthrough a gel filtration column to remove small organic molecules andlow MW oligomers. Later the crude polymer passed through a Tangentialflow filtration system equipped with a 100K MWCO membrane. It is washedusing 20% ethanol until the absorption of the filtrate diminishes.

Method 3: In a round bottom flask both the dibromo dihydrophenanthreneand diboronic dihydrophanenthrene monomers (1:1) were taken anddissolved in THF-water (4:1) mixture containing 10 equivalent of K₂CO₃and 3% Pd(PPh₃)₄. The reaction mixture was put on a Schlenk line and wasdegassed with three freeze-pump-thaw cycles and then heated to 80deg C.under nitrogen with vigorous stirring for 18 hours. Later to thereaction mixture, a capping agent (selected from G1) containingappropriate functional group was added via a cannula under excessnitrogen pressure and 3 hours later the second capping agent (selectedfrom G2) added. After the reaction the crude reaction mixture wasevaporated off and passed through a gel filtration column to removesmall organic molecules and low MW oligomers. Later the crude polymerpassed through a Tangential flow filtration system equipped with a 100KMWCO membrane. It is washed using 20% ethanol until the absorption ofthe filtrate diminishes.

Method 4: Alternatively the polymerization can be done byself-polymerizing a bromo-boronic ester of dihydrophenanthrene molecule.In a round bottom flask dihydrophenanthrene bromoboronic ester was takenand dissolved in THF-water (4:1) mixture containing 10 equivalent ofK₂CO₃ and 3% Pd(PPh₃)₄. The reaction mixture was put on a Schlenk lineand was degassed with three freeze-pump-thaw cycles and then heated to80deg C. under nitrogen with vigorous stirring for 18 hours. Later tothe reaction mixture, a capping agent (selected from G1) containingappropriate functional group was added via a cannula under excessnitrogen pressure and 3 hours later the second capping agent (selectedfrom G2) added. After the reaction the crude reaction mixture wasevaporated off and passed through a gel filtration column to removesmall organic molecules and low MW oligomers. Later the crude polymerpassed through a Tangential flow filtration system equipped with a 100KMWCO membrane. It is washed using 20% ethanol until the absorption ofthe filtrate diminishes.

Example 2: Preparation of Fluorene-DHP Copolymer Complex

Method 1: In a round bottom flask both the dibromo DHP and diboronicfluorene monomers (1:1) were taken in (DMF-water) mixture and purgedwith nitrogen for 10 minutes. Under nitrogen about 20 equivalent of CsFand 10% of Pd(OAc)2 were mixed and heated at 80deg Celsius.Polymerization was monitored using UV-Vis spectroscopy and SECchromatography. Later to the reaction mixture, a capping agent (selectedfrom G1) containing appropriate functional group was added and 3 hourslater the second capping agent (selected from G2) added. After thereaction the crude reaction mixture was evaporated off and passedthrough a gel filtration column to remove small organic molecules andlow MW oligomers. Later the crude polymer passed through a Tangentialflow filtration system equipped with a 100K MWCO membrane. It is washedusing 20% ethanol until the absorption of the filtrate diminishes.

Method 2: In a round bottom flask both the dibromo fluorene anddiboronic DHP monomers (1:1) were taken in (DMF-water) mixture andpurged with nitrogen for 10 minutes. Under nitrogen about 20 equivalentof CsF and 10% of Pd(OAc)2 were mixed and heated at 80deg celcius.Polymerization was monitored using UV-Vis spectroscopy and SECchromatography. Later to the reaction mixture, a capping agent (selectedfrom G1) containing appropriate functional group was added and 3 hourslater the second capping agent (selected from G2) added. After thereaction the crude reaction mixture was evaporated off and passedthrough a gel filtration column to remove small organic molecules andlow MW oligomers. Later the crude polymer passed through a Tangentialflow filtration system equipped with a 100K MWCO membrane. It is washedusing 20% ethanol until the absorption of the filtrate diminishes.

Method 3: In a round bottom flask both the dibromo dihydrophenanthreneand diboronic fluorene monomers (1:1) were taken and dissolved inTHF-water (4:1) mixture containing 10 equivalent of K₂CO₃ and 3%Pd(PPh₃)₄. The reaction mixture was put on a Schlenk line and wasdegassed with three freeze-pump-thaw cycles and then heated to 80deg C.under nitrogen with vigorous stirring for 18 hours. Later to thereaction mixture, a capping agent (selected from G1) containingappropriate functional group was added via a cannula under excessnitrogen pressure and 3 hours later the second capping agent (selectedfrom G2) added. After the reaction the crude reaction mixture wasevaporated off and passed through a gel filtration column to removesmall organic molecules and low MW oligomers. Later the crude polymerpassed through a Tangential flow filtration system equipped with a 100KMWCO membrane. It is washed using 20% ethanol until the absorption ofthe filtrate diminishes.

Method 4: In a round bottom flask dibromo fluorene and diboronicdihydrophenanthrene monomers (1:1) were taken and dissolved in THF-water(4:1) mixture containing 10 equivalent of K₂CO₃ and 3% Pd(PPh3)4. Thereaction mixture was put on a Schlenk line and was degassed with threefreeze-pump-thaw cycles and then heated to 80deg C. under nitrogen withvigorous stirring for 18 hours. Later to the reaction mixture, a cappingagent (selected from G1) containing appropriate functional group wasadded via a cannula under excess nitrogen pressure and 3 hours later thesecond capping agent (selected from G2) added. After the reaction thecrude reaction mixture was evaporated off and passed through a gelfiltration column to remove small organic molecules and low MWoligomers. Later the crude polymer passed through a Tangential flowfiltration system equipped with a 100K MWCO membrane. It is washed using20% ethanol until the absorption of the filtrate diminishes.

Example 3 Comparison of Fluorescence Emission Spectra

Comparison of fluorescence emission spectra of fluorene (Fl-Fl),dihydrophenanthrene (DHP-DHP) and fluorene-DHP (DHP-Fl) polymers wereundertaken. DHP containing polymers show a marked difference in theirfluorescence maxima which is at 426-428 nm, whereas the fluorene basedpolymers show a maxima of 421 nm (FIG. 1).

Example 4 Comparison of Absorption Spectra

The absorption spectra of both fluorene (Fl-Fl) polymer anddihydrophenanthrene (DHP-DHP) polymer were measured. The graph showsabsorption of the DHP-DHP polymer (black curve) at 390 and 410 nm,whereas the Fl-Fl (grey curve) polymer shows the maxima around 400 nm.Samples were measured under different concentration (FIG. 2).

Example 5 CD4 Signal to Noise Ratio

The flow cytometric analysis of lysed whole blood stained with the newpolymers-labeled anti-human CD4 and Pacific Blue-labeled CD4 wasundertaken. The positive signal intensity of polymer dyes were nearly 5times higher than Pacific Blue (FIG. 3).

Example 6

Polymers of the present invention were found to possess certain physicaland chemical characteristics of absorption, fluorescence, brightness,molecular weight, polydispersity, dye to protein ratio when conjugatedto an antibody etc. The preferred ranges of these parameters are shownin the table of FIG. 4.

The excitation and emission spectra of tandem polymers was measured.Excitation was carried out at the polymer maxima (405 nm) and theemissions observed from the various acceptor dyes attached to thebackbone (FIG. 5).

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, and patentapplications cited herein are hereby incorporated by reference in theirentirety for all purposes.

What is claimed is:
 1. A water soluble fluorescent polymer having thestructure of Formula I:

wherein; each X is independently selected from the group consisting of aC and Si; each Y is independently selected from the group consisting ofa bond, CR¹R², and SiR¹R²; when Y is a bond X is directly bonded to bothrings; each R¹ is independently selected from the group consisting ofpolyethylene glycol (PEG), ammonium alkyl salt, ammonium alkyloxy salt,ammonium oligoether salt, sulfonate alkyl salt, sulfonate alkoxy salt,sulfonate oligoether salt, sulfonamido oligoether, and

each R² is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, a PEG group, ammonium alkyl salt, ammonium alkyloxysalt, ammonium oligoether salt, sulfonate alkyl salt, sulfonate alkoxysalt, sulfonate oligoether salt, sulfonamido oligoether, and

each R³ is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, and a PEG group; each Z is independently selectedfrom the group consisting of C, O, and N; each Q is independentlyselected from the group consisting of a bond, NH, NR⁴, and CH₂; each Mis independently an electron rich linker unit capable of altering thepolymer band gap and is evenly or randomly distributed along the polymermain chain and is each independently selected from the group consistingof

wherein, each R⁴ is a non-ionic side group capable of impartingsolubility in water in excess if 10 mg/mL and is each independentlyselected from the group consisting of halogen, hydroxyl, C₁-C₁₂ alkyl,C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁-C₁₂ haloalkyl,C₁-C₁₂ alkoxy, C₂-C₁₈ (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino,(CH₂)_(x′)(OCH₂—CH₂)_(y′)OCH₃ where each x′ is independently an integerfrom 0-20; each y′ is independently an integer from 0-50, and a C₂-C₁₈(hetero)aryl group; each optional linker L is an aryl or hetroaryl groupevenly or randomly distributed along the polymer main chain and aresubstituted with one or more pendant chains terminated with a functionalgroup selected from the group consisting of amine, carbamate, carboxylicacid, carboxylate, maleimide, activated ester, N-hydroxysuccinimidyl,hydrazine, hydrazide, hydrazone, azide, alkyne, aldehyde, thiol, andprotected groups thereof for conjugation to another substrate, acceptordye, molecule or binding agent; G¹ and G² are each independentlyselected from the group consisting of hydrogen, halogen, alkyne,optionally substituted aryl, optionally substituted heteroaryl, halogensubstituted aryl, silyl, diazonium salt, triflate, acetyloxy, azide,sulfonate, phosphate, boronic acid substituted aryl, boronic estersubstituted aryl, boronic ester, boronic acid, optionally substituteddihydrophenanthrene (DHP), optionally substituted fluorene, aryl orhetroaryl substituted with one or more pendant chains terminated with afunctional group selected from amine, carbamate, carboxylic acid,carboxylate, maleimide, activated ester, N-hydroxysuccinimidyl,hydrazine, hydrazide, hydrazone, azide, alkyne, aldehyde, thiol, andprotected groups thereof for conjugation to a substrate, or a bindingagent; a, c, and d define the mol % of each unit within the structurewhich each can be evenly or randomly repeated and where a is a mol %from 10 to 100%, c is a mol % from 0 to 90%, and each d is a mol % from0 to 25%; each b is independently 0 or 1; m is an integer from 1 toabout 10,000; and each n is independently an integer from 1 to
 20. 2.The polymer of claim 1, wherein the polymer has the structure of FormulaII:


3. The polymer of claim 1, wherein the polymer has the structure ofFormula III:

wherein, each f is independently an integer from 0 to 50 and each R⁵ isindependently selected from the group consisting of H, C₁-C₁₂ alkyl,C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁-C₁₂ haloalkyl,C₁-C₁₂ alkoxy, C₂-C₁₈ (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino, andC₁-C₁₂ alkoxy.
 4. The polymer of claim 1, wherein the polymer has thestructure of Formula IV:


5. The polymer of claim 1, wherein the polymer has the structure ofFormula V:


6. The polymer of claim 1, wherein the polymer is a copolymer and hasthe structure of Formula VI:

wherein g and a together is a mol % from 10 to 100%.
 7. The polymer ofclaim 1, wherein the polymer is a copolymer and has the structure ofFormula VII:

wherein, each g and a together is a mol % from 10 to 100%; and each f isindependently an integer from 0 to 50 and each R⁵ is independentlyselected from the group consisting of H, C₁-C₁₂ alkyl, C₂-C₁₂ alkene,C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁-C₁₂ haloalkyl, C₁-C₁₂ alkoxy,C₂-C₁₈ (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino, and C₁-C₁₂ alkoxy. 8.The polymer of claim 1, wherein the polymer is a copolymer and has thestructure of Formula VIII:


9. The polymer of claim 1, wherein the polymer is a copolymer and hasthe structure of Formula IX:


10. The polymer of claim 1 wherein L is each independently selected fromthe group consisting of

wherein, each R⁶ is independently selected from the group consisting ofH, OH, SH, NHCOO-t-butyl, (CH₂)_(n)COOH, (CH₂)_(n)COOCH₃, (CH₂)_(n)NH₂,(CH₂)_(n)NH—(CH₂)_(n)—CH₃, (CH₂)_(n)NHCOOH,(CH₂)_(n)NHCO—(CH₂)_(n)—CO—(CH₂)_(n)—CH₃, (CH₂)_(n)NHCOO—(CH₂)_(n)—CH₃,(CH₂)_(n)NHCOOC(CH₃)₃, (CH₂)_(n)NHCO(C₃-C₁₂)cycloalkyl,(CH₂)_(n)NHCO(CH₂CH₂O)_(f), (CH₂)_(n)NHCO(CH₂)_(n)COOH,(CH₂)_(n)NHCO(CH₂)_(n)COO(CH₂)_(n)CH₃, (CH₂)_(n)(OCH₂CH₂)_(f)OCH₃,N-maleimide, halogen, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl,C₁-C₁₂ halo alkyl, C₁-C₁₂ (hetero)aryl, C₁-C₁₂ (hetero)arylamino, andbenzyl optionally substituted with one or more halogen, hydroxyl, C₁-C₁₂alkoxy, or (OCH₂CH₂)_(f)OCH₃; each f is independently an integer from 0to 50; and each n is independently an integer from 1 to
 20. 11. Thepolymer of claim 1, wherein G¹ and G² are each independently selectedfrom the group consisting of optionally substituted dihydrophenanthrene(DHP), optionally substituted fluorene, aryl substituted with one ormore pendant chains terminated with a functional group, and a hetroarylsubstituted with one or more pendant chains terminated with a functionalgroup.
 12. The polymer of claim 1, wherein G¹ and G² are eachindependently selected from the group consisting of

wherein, each R⁶ is independently selected from the group consisting ofH, OH, SH, NHCOO-t-butyl, (CH₂)_(n)COOH, (CH₂)_(n)COOCH₃, (CH₂)_(n)NH₂,(CH₂)_(n)NH—(CH₂)_(n)—CH₃, (CH₂)_(n)NHCOOH,(CH₂)_(n)NHCO—(CH₂)_(n)—CO—(CH₂)_(n)—CH₃, (CH₂)_(n)NHCOO—(CH₂)_(n)—CH₃,(CH₂)_(n)NHCOOC(CH₃)₃, (CH₂)_(n)NHCO(C₃-C₁₂)cycloalkyl,(CH₂)_(n)NHCO(CH₂CH₂O)_(f), (CH₂)_(n)NHCO(CH₂)_(n)COOH,(CH₂)_(n)NHCO(CH₂)_(n)COO(CH₂)_(n)CH₃, (CH₂)_(n)(OCH₂CH₂)_(f)OCH₃,N-maleimide, halogen, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl,C₁-C₁₂ halo alkyl, C₁-C₁₂ (hetero)aryl, C₁-C₁₂ (hetero)arylamino, andbenzyl optionally substituted with one or more halogen, hydroxyl, C₁-C₁₂alkoxy, or (OCH₂CH₂)_(f)OCH₃; each f is independently an integer from 0to 50; and each n is independently an integer from 1 to
 20. 13. Thepolymer of claim 1, further comprising a binding agent linked to saidpolymer.
 14. The polymer of claim 13, wherein the binding agent is anantibody.
 15. A method for detecting an analyte in a sample comprising:providing a sample that is suspected of containing the analyte;contacting the sample with a binding agent conjugated to a water solublepolymer having the structure of Formula I:

wherein; each X is independently selected from the group consisting of aC and Si; each Y is independently selected from the group consisting ofa bond, CR¹R², and SiR¹R²; when Y is a bond X is directly bonded to bothrings; each R¹ is independently selected from the group consisting ofPEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoethersalt, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoethersalt, sulfonamido oligoether, and

each R² is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, a PEG group, ammonium alkyl salt, ammonium alkyloxysalt, ammonium oligoether salt, sulfonate alkyl salt, sulfonate alkoxysalt, sulfonate oligoether salt, sulfonamido oligoether, and

each R³ is independently selected from the group consisting of H, alkyl,alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl,(hetero)arylamino, and a PEG group; each Z is independently selectedfrom the group consisting of C, O, and N; each Q is independentlyselected from the group consisting of a bond, NH, NR⁴, and CH₂; each Mis independently an electron rich linker unit capable of altering thepolymer band gap and is evenly or randomly distributed along the polymermain chain and is each independently selected from the group consistingof

wherein, each R⁴ is a non-ionic side group capable of impartingsolubility in water in excess if 10 mg/mL and is each independentlyselected from the group consisting of halogen, hydroxyl, C₁-C₁₂ alkyl,C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁-C₁₂ haloalkyl,C₁-C₁₂ alkoxy, C₂-C₁₈ (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino,(CH₂)_(x′)(OCH₂—CH₂)_(y′)OCH₃ where each x′ is independently an integerfrom 0-20; each y′ is independently an integer from 0-50, and a C₂-C₁₈(hetero)aryl group; each optional linker L is an aryl or hetroaryl groupevenly or randomly distributed along the polymer main chain and aresubstituted with one or more pendant chains terminated with a functionalgroup selected from the group consisting of amine, carbamate, carboxylicacid, carboxylate, maleimide, activated ester, N-hydroxysuccinimidyl,hydrazine, hydrazid, hydrazone, azide, alkyne, aldehyde, thiol, andprotected groups thereof for conjugation to another substrate, acceptordye, molecule or binding agent; G¹ and G² are each independentlyselected from the group consisting of hydrogen, halogen, alkyne,optionally substituted aryl, optionally substituted heteroaryl, halogensubstituted aryl, silyl, diazonium salt, triflate, acetyloxy, azide,sulfonate, phosphate, boronic acid substituted aryl, boronic estersubstituted aryl, boronic ester, boronic acid, optionally substituteddihydrophenanthrene (DHP), optionally substituted fluorene, aryl orhetroaryl substituted with one or more pendant chains terminated with afunctional group selected from amine, carbamate, carboxylic acid,carboxylate, maleimide, activated ester, N-hydroxysuccinimidyl,hydrazine, hydrazide, hydrazone, azide, alkyne, aldehyde, thiol, andprotected groups thereof for conjugation to a substrate or bindingagent; a, c, and d define the mol % of each unit within the structurewhich each can be evenly or randomly repeated and where a is a mol %from 10 to 100%, c is a mol % from 0 to 90%, and each d is a mol % from0 to 25%; each b is independently 0 or 1; m is an integer from 1 toabout 10,000; and each n is independently an integer from 1 to 20; andwherein the binding agent is capable of interacting with the analyte ora target-associated biomolecule.
 16. The method of claim 15, wherein thebinding agent is a protein, peptide, affinity ligand, antibody, antibodyfragment, sugar, lipid, nucleic acid or an aptamer.
 17. The method ofclaim 15, wherein the binding agent is an antibody.
 18. The method ofclaim 17, wherein the method is configured for flow cytometry.
 19. Themethod of claim 17, wherein the binding agent is bound to a substrate.20. The method of claim 17, wherein the analyte is a protein expressedon a cell surface.
 21. The method of claim 17, wherein the method isconfigured as an immunoassay.
 22. The assay method of claim 17, whereinthe method further comprises providing additional binding agents fordetecting additional analytes simultaneously.